How to bake all animation from ik to fk in blender2.66
I made a Blender Addon that does exactly this.

It generates a new mesh and FK rig, so that your original one remains completely unchanged.

So you can simply export the rig that the Addon generates and then delete it. When you need to export again, just use it to regenerate a new FK rig.

It's open source on GitHub - https://github.com/chinedufn/blender-iks-to-fks

Hope it helps!